Summary
Annotation of plant genomic sequences can be separated into structural and functional annotation. Structural annotation is the foundation of all genomics as without accurate gene models understanding gene function or evolution of genes across taxa can be impeded. Structural annotation is dependent on sensitive, specific computational programs and deep experimental evidence to identify gene features within genomic DNA. Functional annotation is highly dependent on sequence similarity to other known genes or proteins as the majority of initial “first-pass” functional annotation on a genomic scale is transitive. Coupling structural and functional annotation across genomes in a comparative manner promotes more accurate annotation as well as an understanding of gene and genome evolution. With the increasing availability of plant genome sequence data, the value of comparative annotation will increase. As with any new field, methodologies are evolving for genome annotation and will improve in the future.
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References
Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and Wheeler, D.L. (2005) GenBank. Nucleic Acids Res. 33, D34–D38.
Fickett, J.W. (1996) The gene identification problem: an overview for developers. Comput. Chem. 20, 103–118.
Yao, H., Guo, L., Fu, Y., Borsuk, L.A., Wen, T.J., Skibbe, D.S., Cui, X., Scheffler, B.E., Cao, J., Emrich, S.J., et al. (2005) Evaluation of five ab initio gene prediction programs for the discovery of maize genes. Plant Mol. Biol. 57, 445–460.
Salamov, A.A. and Solovyev, V.V. (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10, 516–522.
Lomsadze, A., Ter-Hovhannisyan, V., Chernoff, Y.O., and Borodovsky, M. (2005) Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Res. 33, 6494–6506.
Mathe, C., Sagot, M.F., Schiex, T., and Rouze, P. (2002) Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res. 30, 4103–4117.
Jurka, J., Kapitonov, V.V., Pavlicek, A., Klonowski, P., Kohany, O., and Walichiewicz, J. (2005) Repbase update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462–467.
Ouyang, S. and Buell, C.R. (2004) The TIGR plant repeat databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res. 32, D360–D363.
Bedell, J.A., Korf, I., and Gish, W. (2000) MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics 16, 1040–1041.
Childs, K., Hamilton, J., Zhu, W., Ly, E., Cheung, F., Wu, H., Rabinowicz, P.D., Town, C.D., Buell, C.R., and Chan, A.P. (2007) The TIGR plant transcript assemblies database. Nucleic Acids Res. 35(Database issue), D846–D851.
Gish, W. and States, D.J. (1993) Identification of protein coding regions by database similarity search. Nat. Genet. 3, 266–272.
Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.C., Estreicher, A., Gasteiger, E., Martin, M.J., Michoud, K., O’Donovan, C., Phan, I., et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31, 365–370.
Bairoch, A., Apweiler, R., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., et al. (2005) The universal protein resource (UniProt). Nucleic Acids Res. 33, D154–D159.
Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L., et al. (2004) The Pfam protein families database. Nucleic Acids Res. 32, D138–D141.
Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bradley, P., Bork, P., Bucher, P., Cerutti, L., et al. (2005) InterPro, progress and status in 2005. Nucleic Acids Res. 33, D201–D205.
Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., and Lopez, R. (2005) InterProScan: protein domains identifier. Nucleic Acids Res. 33, W116–W120.
Lee, V., Camon, E., Dimmer, E., Barrell, D., and Apweiler, R. (2005) Who tangos with GOA?-use of Gene Ontology Annotation (GOA) for biological interpretation of ‘-omics’ data and for validation of automatic annotation tools. In Silico Biol. 5, 5–8.
Haas, B.J., Wortman, J.R., Ronning, C.M., Hannick, L.I., Smith, R.K., Jr. Maiti, R., Chan, A.P., Yu, C., Farzad, M., Wu, D., et al. (2005) Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC Biol. 3, 7.
Berardini, T.Z., Mundodi, S., Reiser, L., Huala, E., Garcia-Hernandez, M., Zhang, P., Mueller, L.A., Yoon, J., Doyle, A., Lander, G., et al. (2004) Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol. 135, 745–755.
Camon, E., Magrane, M., Barrell, D., Lee, V., Dimmer, E., Maslen, J., Binns, D., Harte, N., Lopez, R., and Apweiler, R. (2004) The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res. 32, D262–D266.
Rensink, W.A. and Buell, C.R. (2005) Microarray expression profiling resources for plant genomics. Trends Plant Sci. 10, 603–609.
Ronning, C.M., Stegalkina, S.S., Ascenzi, R.A., Bougri, O., Hart, A.L., Utterbach, T.R., Vanaken, S.E., Riedmuller, S.B., White, J.A., Cho, J., et al. (2003) Comparative analyses of potato expressed sequence tag libraries. Plant Physiol. 131, 419–429.
Journet, E.P., van Tuinen, D., Gouzy, J., Crespeau, H., Carreau, V., Farmer, M.J., Niebel, A., Schiex, T., Jaillon, O., Chatagnier, O., et al. (2002) Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis. Nucleic Acids Res. 30, 5579–5592.
Nakano, M., Nobuta, K., Vemaraju, K., Tej, S.S., Skogen, J.W., and Meyers, B.C. (2006) Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res. 34, D731–D735.
Meyers, B.C., Vu, T.H., Tej, S.S., Ghazal, H., Matvienko, M., Agrawal, V., Ning, J., and Haudenschild, C.D. (2004) Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing. Nat. Biotechnol. 22, 1006–1011.
Cheung, F., Haas, B.J., Goldberg, S.M., May, G.D., Xiao, Y., and Town, C.D. (2006) Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology. BMC Genomics 7, 272.
Alonso, J.M., Stepanova, A.N., Leisse, T.J., Kim, C.J., Chen, H., Shinn, P., Stevenson, D.K., Zimmerman, J., Barajas, P., Cheuk, R., et al. (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301, 653–657.
Jeong, D.H., An, S., Park, S., Kang, H.G., Park, G.G., Kim, S.R., Sim, J., Kim, Y.O., Kim, M.K., Kim, S.R., et al. (2006) Generation of a flanking sequence-tag database for activation-tagging lines in japonica rice. Plant J. 45, 123–132.
Greco, R., Ouwerkerk, P.B., Taal, A.J., Favalli, C., Beguiristain, T., Puigdomenech, P., Colombo, L., Hoge, J.H., and Pereira, A. (2001) Early and multiple Ac transpositions in rice suitable for efficient insertional mutagenesis. Plant Mol. Biol. 46, 215–227.
Kumar, C.S., Wing, R.A., and Sundaresan, V. (2005) Efficient insertional mutagenesis in rice using the maize En/Spm elements. Plant J. 44, 879–892.
Kim, C.M., Piao, H.L., Park, S.J., Chon, N.S., Je, B.I., Sun, B., Park, S.H., Park, J.Y., Lee, E.J., Kim, M.J., et al. (2004) Rapid, large-scale generation of Ds transposant lines and analysis of the Ds insertion sites in rice. Plant J. 39, 252–263.
Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A., et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res. 12, 1599–1610.
Rutherford, K., Parkhill, J., Crook, J., Horsnell, T., Rice, P., Rajandream, M.A., and Barrell, B. (2000) Artemis: sequence visualization and annotation. Bioinformatics 16, 944–945.
Acknowledgements
We acknowledge the efforts of the TIGR Bioinformatics department that has made a number of robust annotation tools readily available to our group. Genome annotation is funded by grants to C.R.B from the National Science Foundation (DBI-0218166 and DBI-0321538). Note added in proof. Subsequent to the submission of this chapter, rice genome project at TIGR moved to Michigan State University (new URL http://rice.plantbiology.msu.edu/)
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Ouyang, S., Thibaud-Nissen, F., Childs, K., Zhu, W., Buell, C. (2009). Plant Genome Annotation Methods. In: Gustafson, J., Langridge, P., Somers, D. (eds) Plant Genomics. Methods in Molecular Biology™, vol 513. Humana Press. https://doi.org/10.1007/978-1-59745-427-8_14
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DOI: https://doi.org/10.1007/978-1-59745-427-8_14
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